16S_minimap

STEP 1) Format Taxa file for dictionary

## # A tibble: 6 x 8
##   TAXAID    Domain  phylum    class     order    family   genus   species       
##   <chr>     <chr>   <chr>     <chr>     <chr>    <chr>    <chr>   <chr>         
## 1 AB001445… Bacter… Proteoba… Gammapro… Pseudom… Pseudom… Pseudo… Pseudomonas a…
## 2 KM209255… Bacter… Proteoba… Gammapro… Enterob… Pectoba… Dickeya Dickeya phage…
## 3 HL281554… Bacter… Actinoba… Actinoba… Actinom… Actinom… F0332   unidentified  
## 4 AB002515… Bacter… Firmicut… Bacilli   Lactoba… Strepto… Strept… Streptococcus…
## 5 AB002523… Bacter… Firmicut… Bacilli   Lactoba… Strepto… Strept… Streptococcus…
## 6 JN049487… Bacter… Actinoba… Actinoba… Pseudon… Pseudon… Saccha… actinobacteri…

STEP 2) Abudnace of Bacterial Families in Each Samples

2.1) BC03 Top 10 families Abundances

## [1] "Check if all multi-mapping reads has been summarised into the Lowest Common Ancestor:"

## [1] "Number of current readID in BC03 65014"

## [1] "Number of unique readID in BC03 65014"

## # A tibble: 11 x 3
##    family           Number.Reads Sample
##    <chr>                   <int> <chr> 
##  1 Comamonadaceae          30058 BC03  
##  2 Spirosomaceae            5408 BC03  
##  3 Aeromonadaceae           3854 BC03  
##  4 Alteromonadaceae         2836 BC03  
##  5 Oxalobacteraceae         2731 BC03  
##  6 Erwiniaceae              1986 BC03  
##  7 Pseudomonadaceae         1576 BC03  
##  8 Arcobacteraceae          1500 BC03  
##  9 Rhodocyclaceae           1425 BC03  
## 10 Burkholderiaceae         1237 BC03  
## 11 Other                   12403 BC03

2.1.2) Leptospira in BC03

2.2) BC04 Top 10 families Abundances

## [1] "Check if all multi-mapping reads has been summarised into the Lowest Common Ancestor:"

## [1] "Number of current readID in BC04 65554"

## [1] "Number of unique readID in BC04 65554"

## # A tibble: 1 x 10
##   READID      TAXAID     MAPQ Domain  phylum  class order  species genus family 
##   <chr>       <chr>     <dbl> <chr>   <chr>   <chr> <chr>  <chr>   <chr> <chr>  
## 1 97deda1c-c… CP022538…     0 Bacter… Spiroc… Lept… Lepto… <NA>    Lept… Leptos…

## # A tibble: 11 x 3
##    family             Number.Reads Sample
##    <chr>                     <int> <chr> 
##  1 Aeromonadaceae            51893 BC04  
##  2 Pseudomonadaceae           3898 BC04  
##  3 Chromobacteriaceae         2091 BC04  
##  4 Moraxellaceae              1979 BC04  
##  5 Comamonadaceae             1872 BC04  
##  6 Enterobacteriaceae          897 BC04  
##  7 Exiguobacteraceae           689 BC04  
##  8 Clostridiaceae              517 BC04  
##  9 Bacillaceae                 242 BC04  
## 10 Alteromonadaceae            168 BC04  
## 11 Other                      1308 BC04

2.3) BC05 Top 10 families Abundances

2.4) BC06 Top 10 families Abundances

combined Top 10 families

Mapping Profiling Statistics